Research workbench
Crystal structure of an ancestor of all faviina proteins
Analyse Crystal structure of an ancestor of all faviina proteins in the GL1X research workbench: secondary structure, accessibility, pockets, interfaces, conservation, variants, modifications, peptides, crosslinks and neighbours on the 3D structure.
- PDB
- 4DXI
- Type
- protein
- Length
- 874 residues
- Chains
- 4
- Method
- x-ray diffraction
- Collection
- MolNFT v1 / PDB
- Contract
- 0xDE3723766Bc32dcACD03C17BaA400A7B36837Eba
- Owner
- 0x3396CDB397284571d12822B4ae1189a8E22AAAAA
- Molecule
- Green fluorescent protein
- Ligands
- CRQ, MG
- Pockets
- 12 · best druggability 0.83
Structure
x-ray diffraction · 3 distinct chains · 5% helix, 57% strand (DSSP).
| Chain | Molecule | Type | Residues | Secondary structure | UniProt |
|---|---|---|---|---|---|
| A, D | Green fluorescent protein | protein | 217 | 5% helix, 57% strand | — |
| B | Green fluorescent protein | protein | 221 | 5% helix, 56% strand | — |
| C | Green fluorescent protein | protein | 219 | 5% helix, 57% strand | — |
Ligands and binding sites
- CRQ · [2-(3-carbamoyl-1-imino-propyl)-4-(4-hydroxy-benzylidene)-5-oxo-4,5-dihydro-imidazol-1-yl]-acetic acid · ligand · 4 copies · chains A, B, C, D
- MG · Magnesium ion · metal · chains A, B
Binding sites are the residues within 4.5 Å of a ligand's heavy atoms.
Pockets
12 pockets found on a 1 Å grid, 5 with a druggability of 0.5 or more.
| Volume (ų) | Druggability | Buriedness | Lining residues | Inside | |
|---|---|---|---|---|---|
| 1 | 1072 | 0.83 | 0.85 | 112 | empty |
| 2 | 82 | 0.75 | 0.97 | 25 | CRQ |
| 3 | 74 | 0.75 | 0.98 | 26 | CRQ |
| 4 | 75 | 0.74 | 0.98 | 27 | CRQ |
| 5 | 70 | 0.74 | 0.98 | 27 | CRQ |
Interfaces
6 interfaces between chains.
- C–D · 1445 Ų buried · 27 hydrogen bonds · protein-protein
- A–B · 1443 Ų buried · 28 hydrogen bonds · protein-protein
- A–D · 981 Ų buried · 15 hydrogen bonds · protein-protein
- B–C · 968 Ų buried · 15 hydrogen bonds · protein-protein
- B–D · 16 Ų buried · 0 hydrogen bonds · protein-protein
Modifications
Observed in the structure: 8 cofactor (chromophore).
Compared structures
- 4DXI · Crystal Structure of an Ancestor of All Faviina Proteins · the same entry in another collection · chain A against A, TM-score 1.00
Analyse
- Open in the research workbench: secondary structure, accessibility, pockets, interfaces, conservation, variants, modifications, peptides and crosslinks on the 3D structure
- Elsewhere: RCSB PDB 4DXI · PDBe 4DXI
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